Metadata

We need a csv or excel table with metadata that is also reflected in the filename parts. Click on ‘Code’ in this section to show how it was done.

library(DT)
library(dplyr)
#-------------------------------------------------
# Read filenames from directory
dirinput <-
  'C:/Users/GFraga/Documents/GitHub/CRS_AFFORD/AFFORD_THUMBS/Spring/'
fnames <- dir(dirinput)
ext = '.jpg'
pattern = paste0('^JP*.*',ext,'$')
# Create metadata table
metadata <- as.data.frame(fnames[grepl(pattern, fnames)])
colnames(metadata) <- 'file'

# Fill metadata columns from different filename parts

basenames <- sapply(strsplit(metadata$file, ext), '[[', 1)
basenames_firstpart <- sapply(strsplit(basenames,'_'),'[[',1)


metadata$specID <- sapply(strsplit(basenames, '-'), '[[', 1)
metadata$status <- sapply(strsplit(basenames, '-'), '[[', 2)
metadata$scanID <- sapply(strsplit(basenames_firstpart, '-'), '[[', 3)
metadata$desc <- sapply(strsplit(basenames_firstpart, '-'), function(x) paste(x[-(1:3)], collapse = '-')) # take everything after the first 2 elements of the first part

#metadata$version <- sapply(strsplit(basenames,'-v'), function(x) paste0(x[-(1)],collapse = ''))
#metadata$version <- sapply(metadata$version, function(x) sub('_.*', '', x))

metadata$seq <- sapply(strsplit(sapply(strsplit(basenames, '_rec'), '[[', 1),'_'),function(x) paste(x[-1],collapse=''))

# Move version info from desc to seq 
metadata$desc[which(sapply(metadata$seq, function(x) grepl('v.*',x)))] <- metadata$seq[which(sapply(metadata$seq, function(x) grepl('v.*',x)))]
metadata$seq[which(sapply(metadata$seq, function(x) grepl('v.*',x)))] <- 'inconsistent filename' 

# recording ID 
metadata$rec <- sapply(strsplit(basenames, '_rec'), function(x) paste0('rec',x[(2)]))


# add html component to column with file namens
metadata$pic <- metadata$file
metadata$pic <- paste0('<img src=\'Spring/', metadata$pic, '\' height=\'50\' witdth = \'50\'></img>')


#metadata %>% relocate(file, .after = last_col())

Filenames

Scheme

<specID>_<status>_<scanID><(desc)>_<rec>

Labels

specID: str + num specimen ID (JP01)

status: str specimen status (dead | invivo)

scanID: num + str scan number (1scan or scan1)

desc: OPTIONAL str + num additional description of number of scans, anatomy, state,version,etc

seq: num sequence number (053)

rec: str + num recording identifier (rec00182)

Legend:

<field> required field

<(field)> Optional field

Picture viewer

Compact

# Dynamic table -------------------------------------------------



# Render table (ref https://www.rdocumentation.org/packages/DT/versions/0.28/topics/datatable)
 datatable(
    metadata, filter = "top",
    rownames=FALSE, width="100%",
    class='compact cell-border hover', # CSS classes https://datatables.net/manual/styling/classes
    extensions=c('Buttons','Select','SearchPanes'),
    selection = 'none',
    options=list(dom='Bfrtip', buttons=c('copy','csv','excel','pdf')),
    escape=FALSE
  )

With Filter Panes

# Dynamic table -------------------------------------------------


 datatable(
  metadata, filter = "top",
  rownames=FALSE, width="100%", 
  class='compact cell-border hover', # CSS classes https://datatables.net/manual/styling/classes
  extensions=c('Buttons','Select','SearchPanes'),
  #selection = 'none',
  selection = 1,
  escape = FALSE,
  options = list(dom = 'PBfrtip', buttons=c('copy','csv','excel','pdf'),
                 columnDefs = list(list(
                   searchPanes = list(show = TRUE), 
                   targets = 5
                 ))),
)

With Collapsed Filter Panes

# Dynamic table -------------------------------------------------


datatable(
  metadata, filter = "top",
  rownames=FALSE, width="100%", 
  class='compact cell-border hover', # CSS classes https://datatables.net/manual/styling/classes
  extensions=c('Buttons','Select','SearchPanes'),
  #selection = 'none',
  selection = 1,
  escape = FALSE,
  options = list(
    dom = 'Btip',
    buttons=c('searchPanes','copy','csv','excel','pdf'),
    language = list(searchPanes = list(collapse = "FILTER ROWS")),
    #scrollY = 390,
    #scroller = TRUE,
    columnDefs = list(
      list(searchPanes = list(show = FALSE), targets = 5)
    #  list(searchPanes = list(controls = FALSE), targets = 5)
    )
  ) 
)

Issues

  • Naming: specID includes country, relabel it to <country><specID> ?
  • Hover resizing will have to be adapted if Scroller is TRUE
  • Using tabs remove the TOC
  • Button visibility when having one for “FILTER ROWS’